1) What would native victory conditions be, and how do you stop them simply declaring war on the Europeans as soon as they land?
I would base this on the history, and chiefly I'd be using the Iroqouis as a template, since they are most amenable to fitting in with the rest of the game for various reasons - chiefly that they actually were a power player in the pre-Revolutionary period and made a near-succesful bid to remain on the stage.
At some point, you would develop an alliance with a European civ. Your victory would be in assisting your ally, the mother country, put down the attempted independance of the colony, which would leave you as a power in your own right. The colony would be AI, it would choose when to declare independance and it wouldn't do so until it was well and ready, so you wouldn't be in a position to take steps to thwart the rebellion before it happened. Basically your aim would be to survive the war of independance, possibly you could also choose sides and instead side with the colonists. Perhaps it would depend on some diplomatic factor.
In the meantime, you would be attempting to expand your territory the same as other powers - by defeating other natives and non-allied European colonies. Rather than developing specialists and building your economy that way, your efforts would go into controlling trade routes and developing an export economy - building trading posts at key locations, seizing trade routes from your opponents, etc.
As far as preventing natives from declaring war immediately, well, I wouldn't stop it ... but it would set you back badly. You would be contending with other native powers and it would be advisable to try to form an alliance with some European power as quickly as you could, else you'd be showing up to gunfights with a bow and arrow. It would be important to try to trade with Europeans before your neighbours (or not too long after they start). Native civs which immediately declared war on the first Europeans they encountered would probably be wiped out, either by the European power or by their neighbours. There'd probably only be one European power landing in your immediate area, so if you blew first contact, you wouldn't get another chance until it was too late. In the early game, you'd be more concerned with protecting your Europeans from other native groups seeking to cut off your source of guns and metal weapons.
All just off the top of my head ... there would be other ways of doing it, but that's how I'd do it. It's certainly not impossible to include them, that's just a failure of imagination, which is generally a bad thing in game design.